9KL3 | pdb_00009kl3

CryoEM structure of Pleurocybella porrigens lectin (PPL) in complex with GalNAc

• PDB DOI: https://doi.org/10.2210/pdb9KL3/pdb
• EM Map EMD-62399: EMDB EMDataResource

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Pleurocybella porrigens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-14 Released: 2025-11-19 
• Deposition Author(s): Ishimoto, N., Adachi, D., Kawabata, H., Park, S.Y., Tame, J.R.H., Kamata, K.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.24 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Crystal and Cryo-EM structure of PPL, a novel hexameric R-type lectin from the poisonous mushroom Pleurocybella porrigens.

Adachi, D., Ishimoto, N., Mizutani, K., Takahashi, K., Kubota, R., Kawabata, H., Park, S.Y., Vandebroek, L., Voet, A.R.D., Yamada, M., Ozeki, Y., Fujii, Y., Fujita, H., Tame, J.R.H., Kamata, K.

(2025) Glycobiology 36

• PubMed: 41342409 
• DOI: https://doi.org/10.1093/glycob/cwaf082
• Primary Citation Related Structures: 
  9KL2, 9KL3


• PubMed Abstract: 
  

  Pleurocybella porrigens is a mushroom that grows widely around the temperate northern hemisphere, and was once considered edible, especially in Japan. Following a number of deaths in 2004, investigations revealed the presence of various toxins, including a lectin (PPL) that apparently survives cooking and enters the bloodstream via the stomach. We have cloned PPL and solved its structure by X-ray crystallography and cryo-EM. We report the sugar binding properties of this β-trefoil lectin, which has a novel hexameric structure.

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Organizational Affiliation: 
• Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan.
Center of Quantum Life Science for Structural Therapeutics, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.
Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
Graduate School of NanoBio Sciences, Yokohama City University, 22-2 Seto, Yokohama, Kanagawa 236-0027, Japan.
Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki 859-3298, Japan.
College of Science and Technology, Nihon University, 1-5-1 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 14.85 kDa 
• Atom Count: 1,026 
• Modeled Residue Count: 137 
• Deposited Residue Count: 140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	A	140	Pleurocybella porrigens	Mutation(s): 0
UniProt
Find proteins for B6ZK51 (Pleurocybella porrigens) Explore B6ZK51  Go to UniProtKB:  B6ZK51

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A2G	B [auth A]	2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.24 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Ishimoto, N., Adachi, D., Kawabata, H., Park, S.Y., Tame, J.R.H., Kamata, K.

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Funding Organization	Location	Grant Number
Other private		Y-2023-2-046

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release
  
• Version 1.1: 2025-12-17
  Changes: Data collection, Database references
• Version 1.2: 2025-12-31
  Changes: Data collection, Database references
• Version 1.3: 2026-07-08
  Changes: Data collection, Derived calculations